Contacts of the helix formed by residues 649 - 672 (chain B) in PDB entry 1JB0
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LEU 649 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B TYR* 5.9 0.7 - - - +
636B GLN* 4.3 18.4 - - + +
637B LEU 4.3 2.7 - - - +
640B GLY* 3.5 8.2 - - - -
647B ASN* 2.7 21.3 - - - +
648B ASN* 1.3 91.5 - - - +
650B SER* 1.3 65.6 + - - +
651B VAL 3.2 1.8 - - - -
652B TRP* 3.4 23.3 + - + +
653B ALA* 3.0 23.9 + - - +
733B ALA* 4.1 22.2 - - + +
736B ALA* 4.7 13.5 - - + -
737B ALA* 3.9 28.9 - - + +
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Residues in contact with SER 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ALA 4.0 16.8 + - - -
103B PHE* 3.3 19.4 - - - -
640B GLY* 3.5 22.5 + - - -
641B TYR* 3.9 10.2 - - - -
646B THR* 4.2 5.5 - - - -
647B ASN 2.9 17.0 + - - -
649B LEU* 1.3 77.0 - - - +
651B VAL* 1.3 67.7 + - - +
653B ALA* 3.3 1.6 + - - +
654B TRP* 3.0 24.6 + - - +
1206B CLA 3.6 10.1 - - - +
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Residues in contact with VAL 651 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B PHE* 3.3 30.5 - - + -
113B ASP* 5.4 0.2 - - - +
648B ASN 4.1 7.9 - - - +
650B SER* 1.3 77.1 + - - +
652B TRP* 1.3 62.3 + - + +
654B TRP* 3.0 7.8 + - - +
655B MET* 2.7 35.8 + - - +
1205B CLA 4.0 25.1 - - + -
1206B CLA 3.4 49.4 - - + -
4017B BCR 4.2 12.3 - - + -
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Residues in contact with TRP 652 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B ILE 5.6 0.2 - - - -
116B TYR* 4.1 16.2 + + - -
637B LEU* 3.5 2.8 - - + +
648B ASN 4.2 3.4 + - - -
649B LEU* 3.4 34.5 + - + +
651B VAL* 1.3 89.4 - - + +
653B ALA* 1.3 57.1 + - - +
655B MET* 3.9 21.5 - - + -
656B PHE* 2.8 30.5 + - - +
728B ALA 4.7 0.2 - - - -
729B ALA* 3.2 22.7 - - - +
732B ILE* 3.6 36.2 - - + +
733B ALA* 3.9 24.2 - - + -
1205B CLA 3.5 47.8 - - + -
1224B CLA 4.3 22.9 - - + -
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Residues in contact with ALA 653 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ASN* 4.9 7.2 + - - +
637B LEU* 3.1 32.3 - - - +
638B ILE* 5.0 2.5 - - + -
640B GLY* 4.0 10.8 - - - +
641B TYR* 4.1 15.0 - - + +
649B LEU 3.0 14.3 + - - +
650B SER 3.7 4.3 - - - +
652B TRP* 1.3 76.9 - - - +
654B TRP* 1.3 62.8 + - - +
656B PHE* 3.3 6.1 - - - +
657B LEU* 3.2 26.7 + - - +
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Residues in contact with TRP 654 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ASP 4.3 1.8 - - - -
464A THR* 3.1 31.9 + - - -
467A ALA* 4.4 1.1 - - + -
1022A CLA 3.5 69.9 - - + +
1132A CLA 5.1 0.2 - - + -
641B TYR* 4.0 16.5 - - + -
650B SER 3.0 14.1 + - - +
651B VAL* 3.4 7.4 - - - +
653B ALA* 1.3 74.7 - - - +
655B MET* 1.3 64.3 + - - +
657B LEU* 3.0 6.8 + - - +
658B PHE* 2.8 42.6 + + + +
1206B CLA 3.4 40.1 - - + +
4017B BCR 3.7 46.7 - - + -
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Residues in contact with MET 655 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651B VAL 2.7 19.8 + - - +
652B TRP* 3.8 21.3 - - + +
654B TRP* 1.3 76.2 - - - +
656B PHE* 1.3 53.8 + - - +
658B PHE* 3.2 8.7 - - - +
659B GLY* 2.8 32.4 + - - -
725B LEU* 4.1 28.9 - - + +
729B ALA* 4.1 3.4 - - + -
1205B CLA 3.6 49.8 - - + -
1224B CLA 3.5 25.1 - - + -
4017B BCR 4.0 25.6 - - + -
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Residues in contact with PHE 656 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ASN* 6.2 0.2 - - - -
650A LEU* 3.7 20.6 - - + -
634B SER* 5.0 0.2 - - - -
637B LEU* 3.7 19.7 - - + -
638B ILE* 3.3 31.4 - - + -
652B TRP 2.8 20.2 + - - +
653B ALA* 3.3 9.9 - - - +
655B MET* 1.3 77.4 - - - +
657B LEU* 1.3 60.8 + - + +
659B GLY 3.5 0.3 + - - -
660B HIS* 2.9 38.0 + + - -
726B THR* 3.3 41.4 + - + +
729B ALA* 3.7 9.0 - - + -
730B PHE* 3.9 9.9 - - + -
1021B CLA 3.5 35.9 - + + -
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Residues in contact with LEU 657 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ASP* 3.5 12.1 - - - +
646A ILE* 4.0 13.9 - - + -
647A ASN* 3.6 20.4 - - + +
650A LEU* 3.7 33.4 - - + -
1022A CLA 3.4 42.4 - - + +
641B TYR* 3.3 26.7 - - - +
653B ALA 3.2 9.1 + - - +
654B TRP 3.0 7.6 + - - +
656B PHE* 1.3 75.7 - - + +
658B PHE* 1.3 65.8 + - - +
660B HIS* 3.1 11.3 + - + +
661B LEU* 3.0 18.9 + - - +
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Residues in contact with PHE 658 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A CLA 3.7 36.7 - - + +
654B TRP* 2.8 24.8 + + + +
655B MET* 3.2 12.8 - - - +
657B LEU* 1.3 77.4 - - - +
659B GLY* 1.3 61.6 + - - +
661B LEU* 3.1 6.0 + - + +
662B VAL* 3.0 34.2 + - + +
725B LEU* 3.3 33.9 - - + -
1226B CLA 3.9 14.8 - - + -
1239B CLA 3.5 30.3 - - + -
4017B BCR 3.6 44.2 - - + -
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Residues in contact with GLY 659 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655B MET 2.8 18.3 + - - -
658B PHE* 1.3 73.7 - - - +
660B HIS* 1.3 63.4 + - - +
662B VAL* 3.4 0.6 + - - -
663B TRP* 3.0 21.7 + - - +
722B GLY* 3.2 22.1 - - - -
725B LEU* 4.1 7.0 - - - -
726B THR* 2.9 23.8 - - - -
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Residues in contact with HIS 660 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A LEU* 5.3 2.0 - - + +
1022A CLA 3.0 48.2 - - + +
656B PHE* 2.9 45.1 + + - +
657B LEU* 3.1 13.9 + - + +
659B GLY* 1.3 76.1 - - - +
661B LEU* 1.3 62.1 + - - +
663B TRP* 3.6 1.9 - - - +
664B ALA* 3.1 24.9 + - - +
726B THR* 3.1 29.2 + - + +
1021B CLA 2.4 57.2 + + + -
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Residues in contact with LEU 661 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456A PHE* 4.3 17.0 - - + -
1022A CLA 3.7 65.9 - - + +
657B LEU 3.0 11.5 + - - +
658B PHE* 3.1 9.8 + - + +
660B HIS* 1.3 75.8 - - - +
662B VAL* 1.3 55.7 + - - +
664B ALA* 3.4 1.7 + - - -
665B THR* 2.7 39.5 + - - +
1023B CLA 3.9 16.4 - - + +
1239B CLA 3.5 39.9 - - + -
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Residues in contact with VAL 662 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B PHE* 3.0 36.5 + - + +
659B GLY* 4.0 3.1 - - - +
661B LEU* 1.3 72.8 - - - +
663B TRP* 1.3 65.1 + - - +
665B THR* 3.3 7.8 + - - -
666B GLY 3.1 16.5 + - - -
718B HIS* 3.2 42.2 - - + +
721B VAL* 4.0 11.9 - - + -
722B GLY* 3.8 11.2 - - - +
1239B CLA 3.6 38.8 - - + -
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Residues in contact with TRP 663 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A TRP* 3.7 15.0 - + - -
1011A CLA 4.1 3.1 - - + -
1022A CLA 3.2 37.9 - + + -
659B GLY 3.0 17.8 + - - +
660B HIS 3.6 2.5 - - - +
662B VAL* 1.3 77.9 - - - +
664B ALA* 1.3 73.2 + - - +
666B GLY* 3.0 12.1 + - - -
667B PHE* 3.3 49.4 + + - -
718B HIS 4.0 8.3 - - - -
719B PHE* 3.2 50.9 - + - +
722B GLY* 3.9 4.0 - - - -
723B TYR* 4.1 9.2 - - - -
1012B CLA 3.6 11.4 - - + -
1021B CLA 3.2 59.3 - + + +
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Residues in contact with ALA 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A CLA 3.3 41.5 - - + +
660B HIS 3.1 11.3 + - - +
661B LEU 4.0 0.2 - - - +
663B TRP* 1.3 86.7 - - - +
665B THR* 1.3 60.5 + - - +
667B PHE* 3.1 24.8 + - - +
668B MET 3.8 2.6 + - - -
1023B CLA 3.2 29.5 - - + +
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Residues in contact with THR 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B LEU 2.7 22.1 + - - -
662B VAL* 3.6 7.8 - - - -
663B TRP 3.1 0.4 - - - -
664B ALA* 1.3 78.3 - - - +
666B GLY* 1.3 60.7 + - - +
668B MET* 3.1 27.8 + - + +
669B PHE* 3.4 11.7 - - + -
718B HIS* 3.6 21.3 - - + +
1023B CLA 3.2 28.1 - - + +
1239B CLA 3.7 35.0 - - + +
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Residues in contact with GLY 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B VAL 3.1 6.3 + - - -
663B TRP 3.0 9.5 + - - -
665B THR* 1.3 76.0 - - - +
667B PHE* 1.3 63.0 + - - +
668B MET 3.1 0.7 + - - -
669B PHE* 3.2 3.9 + - - -
670B LEU* 3.1 31.5 + - - +
715B GLY* 3.6 14.1 - - - -
718B HIS* 3.4 23.7 - - - +
719B PHE* 4.2 1.3 - - - -
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Residues in contact with PHE 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A TRP* 3.8 15.0 - + - -
687A LEU* 3.7 34.5 - - + -
691A PHE* 4.0 15.0 - + - -
735A TYR* 4.6 5.8 - + - -
1022A CLA 4.2 9.4 - - + -
663B TRP* 3.3 61.7 - + - -
664B ALA* 3.1 16.9 + - + +
666B GLY* 1.3 78.5 - - - +
668B MET* 1.3 62.1 + - - +
670B LEU* 4.3 6.7 - - - -
671B ILE* 3.0 43.4 + - + +
719B PHE* 3.7 16.8 - + - -
1023B CLA 3.3 14.7 - - + +
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Residues in contact with MET 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664B ALA 3.8 0.6 + - - -
665B THR* 3.1 13.8 + - + +
666B GLY 3.1 1.0 - - - -
667B PHE* 1.3 78.5 - - - +
669B PHE* 1.3 73.6 + - + +
672B SER* 2.8 35.2 + - - +
677B TRP* 4.2 4.7 - - + -
1023B CLA 2.6 88.1 - - + +
1239B CLA 3.8 32.1 - - + -
2002B PQN 3.4 24.7 - - + +
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Residues in contact with PHE 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B THR* 3.4 25.6 - - + -
666B GLY* 3.2 6.0 + - - -
668B MET* 1.3 80.8 - - + +
670B LEU* 1.3 60.7 + - - +
672B SER 3.3 11.1 - - - +
673B TRP* 4.3 3.5 + - - -
706B LEU* 3.9 20.9 - - + -
711B ALA* 3.5 30.6 - - + +
712B ARG* 5.4 0.2 - - - -
714B VAL* 4.0 17.7 - - + -
715B GLY* 3.6 10.3 - - - -
718B HIS* 3.9 20.0 - + - -
1239B CLA 3.5 39.9 - + + -
2002B PQN 3.2 49.2 - + + -
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Residues in contact with LEU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A LEU 3.2 12.4 - - - +
691A PHE* 3.6 35.0 - - + -
583B TYR* 3.2 40.0 + - + +
587B PHE* 3.7 24.0 - - + -
666B GLY 3.1 24.0 + - - +
667B PHE 4.0 0.7 - - - +
669B PHE* 1.3 77.9 - - - +
671B ILE* 1.3 57.5 + - - +
673B TRP* 3.0 18.6 + - - +
712B ARG* 4.0 7.2 - - - +
715B GLY* 3.8 13.2 - - - +
716B LEU 3.8 13.5 - - - +
719B PHE* 4.3 6.5 - - + -
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Residues in contact with ILE 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A GLN* 3.1 19.8 + - - +
596A PHE* 4.0 14.3 - - + -
597A LEU* 4.8 0.2 - - + -
600A PHE* 3.8 42.6 - - + -
687A LEU* 5.0 0.2 - - + -
690A LEU* 4.1 21.5 - - + +
691A PHE* 3.7 26.2 - - + -
735A TYR* 4.5 5.6 - - + -
667B PHE* 3.0 34.3 + - + +
670B LEU* 1.3 78.1 - - - +
672B SER* 1.3 62.1 + - - +
673B TRP* 3.4 4.2 + - - -
1023B CLA 3.8 20.9 - - + -
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Residues in contact with SER 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588A GLN* 3.6 5.2 - - - -
597A LEU* 3.6 27.4 - - - -
668B MET* 2.8 21.8 + - - +
669B PHE 3.3 5.0 - - - +
671B ILE* 1.3 74.8 - - - +
673B TRP* 1.3 68.7 + - - +
677B TRP* 2.9 30.0 + - - -
1023B CLA 4.4 11.9 - - - +
2002B PQN 3.0 19.1 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il